conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484492520 236 RIILIKKKSNNSDDSNaYRPITLASCIAKIKDRMIKRRVEWWIENNQLlpKSQFGFRKGLSTQDSLSIFSTDIHLAFSRN 315
Cdd:cd01650     3 RIILIPKKGKPSDPKN-YRPISLLSVLYKLLEKILANRLRPVLEENIL--PNQFGFRPGRSTTDAILLLREVIEKAKEKK 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1484492520 316 TYVVALFCDIKRAYDNVVPGKLAGSLvhaGLP 347
Cdd:cd01650    80 KSLVLVFLDFEKAFDSVDHEFLLKAL---GVR 108

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484492520 236 RIILIKKKSNNSDDSNaYRPITLASCIAKIKDRMIKRRVEWWIENNQLlpKSQFGFRKGLSTQDSLSIFSTDIHLAFSRN 315
Cdd:cd01650     3 RIILIPKKGKPSDPKN-YRPISLLSVLYKLLEKILANRLRPVLEENIL--PNQFGFRPGRSTTDAILLLREVIEKAKEKK 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1484492520 316 TYVVALFCDIKRAYDNVVPGKLAGSLvhaGLP 347
Cdd:cd01650    80 KSLVLVFLDFEKAFDSVDHEFLLKAL---GVR 108

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1484492520   1 MHKGDDLAKHVTNFCETAAKLNDIGIVVPHEMLVTLLM 38
Cdd:pfam14223  53 MKEGESVLEHINKFEELVNKLSALGVEISDEDLVVKLL 90

RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1484492520 236 RIILIKKKSNNSDDSNaYRPITLASCIAKIKDRMIKRRVEWWIENNQLlpKSQFGFRKGLSTQDSLSIFSTDIHLAFSRN 315
Cdd:cd01650     3 RIILIPKKGKPSDPKN-YRPISLLSVLYKLLEKILANRLRPVLEENIL--PNQFGFRPGRSTTDAILLLREVIEKAKEKK 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1484492520 316 TYVVALFCDIKRAYDNVVPGKLAGSLvhaGLP 347
Cdd:cd01650    80 KSLVLVFLDFEKAFDSVDHEFLLKAL---GVR 108

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1484492520   1 MHKGDDLAKHVTNFCETAAKLNDIGIVVPHEMLVTLLM 38
Cdd:pfam14223  53 MKEGESVLEHINKFEELVNKLSALGVEISDEDLVVKLL 90